Starting phenix.real_space_refine on Sat Aug 8 05:54:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vwa_65392/08_2026/9vwa_65392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vwa_65392/08_2026/9vwa_65392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vwa_65392/08_2026/9vwa_65392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vwa_65392/08_2026/9vwa_65392.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vwa_65392/08_2026/9vwa_65392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vwa_65392/08_2026/9vwa_65392.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 16384 2.51 5 N 4384 2.21 5 O 4936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25832 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "B" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "C" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "D" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "E" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "F" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "G" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Chain: "H" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3229 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 395} Time building chain proxies: 5.61, per 1000 atoms: 0.22 Number of scatterers: 25832 At special positions: 0 Unit cell: (152.88, 153.92, 93.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4936 8.00 N 4384 7.00 C 16384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6064 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 8 sheets defined 65.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 removed outlier: 3.505A pdb=" N GLU A 8 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 36 through 47 removed outlier: 4.025A pdb=" N ASP A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 43 " --> pdb=" O MET A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 71 through 90 removed outlier: 3.781A pdb=" N HIS A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.758A pdb=" N ALA A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.504A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 removed outlier: 3.572A pdb=" N GLU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 225 removed outlier: 3.570A pdb=" N TYR A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 221 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.549A pdb=" N VAL A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.719A pdb=" N GLN A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 291 removed outlier: 3.599A pdb=" N LYS A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 322 removed outlier: 3.868A pdb=" N ALA A 309 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 345 removed outlier: 3.655A pdb=" N TYR A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.849A pdb=" N ASN A 353 " --> pdb=" O ASN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.528A pdb=" N ALA A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.823A pdb=" N TYR A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 18 removed outlier: 3.755A pdb=" N ASN B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 21 No H-bonds generated for 'chain 'B' and resid 19 through 21' Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.950A pdb=" N ASP B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 71 through 90 removed outlier: 3.862A pdb=" N HIS B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.748A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.782A pdb=" N VAL B 118 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.551A pdb=" N ILE B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 200 through 226 removed outlier: 3.514A pdb=" N MET B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 221 " --> pdb=" O HIS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.708A pdb=" N PHE B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 245 removed outlier: 4.033A pdb=" N LYS B 244 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP B 245 " --> pdb=" O LYS B 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 241 through 245' Processing helix chain 'B' and resid 246 through 262 removed outlier: 3.707A pdb=" N ASN B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 291 removed outlier: 3.650A pdb=" N THR B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.745A pdb=" N ALA B 309 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 313 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 345 removed outlier: 3.574A pdb=" N GLU B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.915A pdb=" N ASN B 353 " --> pdb=" O ASN B 350 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 354 " --> pdb=" O LYS B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 354' Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.537A pdb=" N ILE B 363 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'B' and resid 379 through 391 removed outlier: 3.788A pdb=" N ALA B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 removed outlier: 3.530A pdb=" N GLU C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 21 No H-bonds generated for 'chain 'C' and resid 19 through 21' Processing helix chain 'C' and resid 36 through 47 removed outlier: 3.983A pdb=" N ASP C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.834A pdb=" N GLN C 55 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 90 removed outlier: 3.779A pdb=" N HIS C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 104 removed outlier: 3.589A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.747A pdb=" N VAL C 118 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 122 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 removed outlier: 3.516A pdb=" N ALA C 136 " --> pdb=" O GLY C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 removed outlier: 3.578A pdb=" N ILE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 215 through 226 removed outlier: 3.621A pdb=" N ASP C 221 " --> pdb=" O HIS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.708A pdb=" N PHE C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 245 removed outlier: 4.025A pdb=" N LYS C 244 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP C 245 " --> pdb=" O LYS C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 245' Processing helix chain 'C' and resid 246 through 262 removed outlier: 3.774A pdb=" N ASN C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 291 removed outlier: 3.620A pdb=" N THR C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.797A pdb=" N ALA C 309 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 345 removed outlier: 3.589A pdb=" N GLU C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.953A pdb=" N ASN C 353 " --> pdb=" O ASN C 350 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET C 354 " --> pdb=" O LYS C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 366 through 376 Processing helix chain 'C' and resid 381 through 391 removed outlier: 3.582A pdb=" N TYR C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 18 removed outlier: 3.578A pdb=" N GLU D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR D 9 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 17 " --> pdb=" O GLN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 36 through 47 removed outlier: 4.125A pdb=" N ASP D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 43 " --> pdb=" O MET D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 71 through 90 removed outlier: 3.540A pdb=" N ASP D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.511A pdb=" N SER D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.736A pdb=" N ALA D 136 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 137 " --> pdb=" O ASN D 133 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 140 " --> pdb=" O ALA D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 163 removed outlier: 3.547A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 removed outlier: 3.525A pdb=" N GLU D 184 " --> pdb=" O ASP D 180 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.542A pdb=" N GLU D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.540A pdb=" N GLU D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 221 " --> pdb=" O HIS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 239 removed outlier: 3.557A pdb=" N VAL D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 262 removed outlier: 3.939A pdb=" N ASP D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 291 removed outlier: 3.638A pdb=" N LYS D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 322 removed outlier: 3.819A pdb=" N ALA D 309 " --> pdb=" O HIS D 305 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 345 removed outlier: 3.647A pdb=" N TYR D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.959A pdb=" N ASN D 353 " --> pdb=" O ASN D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 381 through 392 removed outlier: 3.531A pdb=" N GLN D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.517A pdb=" N ILE E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 removed outlier: 3.538A pdb=" N GLU E 21 " --> pdb=" O SER E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 removed outlier: 3.958A pdb=" N ASP E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 43 " --> pdb=" O MET E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 71 through 90 removed outlier: 3.812A pdb=" N HIS E 75 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 104 removed outlier: 3.508A pdb=" N SER E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 124 Processing helix chain 'E' and resid 131 through 143 removed outlier: 3.759A pdb=" N ALA E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG E 141 " --> pdb=" O PHE E 137 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU E 143 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 162 Processing helix chain 'E' and resid 179 through 194 removed outlier: 3.659A pdb=" N GLU E 184 " --> pdb=" O ASP E 180 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.503A pdb=" N GLU E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.506A pdb=" N GLU E 220 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 221 " --> pdb=" O HIS E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 240 removed outlier: 3.541A pdb=" N VAL E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER E 238 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 245 removed outlier: 3.832A pdb=" N LYS E 244 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP E 245 " --> pdb=" O LYS E 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 245' Processing helix chain 'E' and resid 246 through 262 removed outlier: 3.611A pdb=" N GLN E 258 " --> pdb=" O ALA E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 291 removed outlier: 3.806A pdb=" N LYS E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 322 removed outlier: 3.750A pdb=" N ALA E 309 " --> pdb=" O HIS E 305 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU E 310 " --> pdb=" O ALA E 306 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG E 322 " --> pdb=" O LYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 345 removed outlier: 3.624A pdb=" N TYR E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.945A pdb=" N ASN E 353 " --> pdb=" O ASN E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 362 removed outlier: 3.639A pdb=" N ALA E 362 " --> pdb=" O PRO E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 376 Processing helix chain 'E' and resid 381 through 392 removed outlier: 3.691A pdb=" N GLN E 385 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR E 390 " --> pdb=" O GLU E 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 18 removed outlier: 3.591A pdb=" N GLU F 8 " --> pdb=" O SER F 4 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN F 15 " --> pdb=" O LYS F 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 36 through 47 removed outlier: 4.002A pdb=" N ASP F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA F 43 " --> pdb=" O MET F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 71 through 90 removed outlier: 3.758A pdb=" N HIS F 75 " --> pdb=" O ASN F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 104 removed outlier: 3.733A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 104 " --> pdb=" O THR F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 124 removed outlier: 3.773A pdb=" N VAL F 118 " --> pdb=" O HIS F 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP F 122 " --> pdb=" O VAL F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 143 removed outlier: 3.694A pdb=" N PHE F 137 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG F 141 " --> pdb=" O PHE F 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 143 " --> pdb=" O ILE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 162 Processing helix chain 'F' and resid 179 through 194 removed outlier: 3.783A pdb=" N LYS F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 226 removed outlier: 3.524A pdb=" N TYR F 214 " --> pdb=" O ASP F 210 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP F 218 " --> pdb=" O TYR F 214 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU F 220 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP F 221 " --> pdb=" O HIS F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.717A pdb=" N PHE F 237 " --> pdb=" O ILE F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 262 removed outlier: 3.790A pdb=" N ASN F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 291 removed outlier: 3.564A pdb=" N ALA F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 322 removed outlier: 3.703A pdb=" N ALA F 309 " --> pdb=" O HIS F 305 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG F 322 " --> pdb=" O LYS F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 345 removed outlier: 3.668A pdb=" N GLN F 335 " --> pdb=" O ARG F 331 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.877A pdb=" N ASN F 353 " --> pdb=" O ASN F 350 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET F 354 " --> pdb=" O LYS F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 350 through 354' Processing helix chain 'F' and resid 357 through 362 removed outlier: 3.867A pdb=" N ALA F 362 " --> pdb=" O PRO F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 376 Processing helix chain 'F' and resid 381 through 391 Processing helix chain 'G' and resid 3 through 18 removed outlier: 3.567A pdb=" N ILE G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN G 15 " --> pdb=" O LYS G 11 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE G 17 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 21 No H-bonds generated for 'chain 'G' and resid 19 through 21' Processing helix chain 'G' and resid 36 through 47 removed outlier: 3.873A pdb=" N ASP G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR G 42 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA G 43 " --> pdb=" O MET G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 71 through 90 removed outlier: 3.800A pdb=" N HIS G 75 " --> pdb=" O ASN G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 104 removed outlier: 3.732A pdb=" N SER G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA G 104 " --> pdb=" O THR G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 124 removed outlier: 3.735A pdb=" N VAL G 118 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP G 122 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 140 Processing helix chain 'G' and resid 156 through 162 Processing helix chain 'G' and resid 179 through 194 Processing helix chain 'G' and resid 200 through 225 removed outlier: 3.858A pdb=" N ASP G 218 " --> pdb=" O TYR G 214 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP G 221 " --> pdb=" O HIS G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 237 removed outlier: 3.739A pdb=" N PHE G 237 " --> pdb=" O ILE G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 245 removed outlier: 4.113A pdb=" N LYS G 244 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP G 245 " --> pdb=" O LYS G 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 241 through 245' Processing helix chain 'G' and resid 246 through 262 Processing helix chain 'G' and resid 270 through 291 removed outlier: 3.587A pdb=" N THR G 282 " --> pdb=" O LYS G 278 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER G 283 " --> pdb=" O LYS G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 322 removed outlier: 3.619A pdb=" N ALA G 309 " --> pdb=" O HIS G 305 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 313 " --> pdb=" O ALA G 309 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 322 " --> pdb=" O LYS G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 345 removed outlier: 3.598A pdb=" N GLU G 342 " --> pdb=" O ARG G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 354 removed outlier: 3.794A pdb=" N ASN G 353 " --> pdb=" O ASN G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 363 removed outlier: 3.785A pdb=" N ALA G 362 " --> pdb=" O PRO G 358 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 363 " --> pdb=" O GLU G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 376 removed outlier: 3.567A pdb=" N THR G 372 " --> pdb=" O THR G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 392 removed outlier: 3.794A pdb=" N ALA G 384 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 18 removed outlier: 3.553A pdb=" N GLU H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR H 9 " --> pdb=" O GLU H 5 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE H 17 " --> pdb=" O GLN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 21 No H-bonds generated for 'chain 'H' and resid 19 through 21' Processing helix chain 'H' and resid 36 through 47 removed outlier: 4.066A pdb=" N ASP H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR H 42 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA H 43 " --> pdb=" O MET H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 71 through 90 removed outlier: 3.691A pdb=" N HIS H 75 " --> pdb=" O ASN H 71 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 104 removed outlier: 3.514A pdb=" N SER H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 124 Processing helix chain 'H' and resid 131 through 143 removed outlier: 3.744A pdb=" N ALA H 136 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE H 137 " --> pdb=" O ASN H 133 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG H 141 " --> pdb=" O PHE H 137 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU H 143 " --> pdb=" O ILE H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 164 removed outlier: 3.501A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 194 removed outlier: 3.569A pdb=" N GLU H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 216 removed outlier: 3.544A pdb=" N GLU H 211 " --> pdb=" O ASP H 207 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR H 214 " --> pdb=" O ASP H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 225 removed outlier: 3.573A pdb=" N GLU H 220 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP H 221 " --> pdb=" O HIS H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 238 removed outlier: 3.562A pdb=" N VAL H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE H 237 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER H 238 " --> pdb=" O VAL H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 262 removed outlier: 3.935A pdb=" N ASP H 252 " --> pdb=" O PRO H 248 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN H 258 " --> pdb=" O ALA H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 272 through 291 removed outlier: 3.673A pdb=" N LYS H 278 " --> pdb=" O ALA H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 322 removed outlier: 3.846A pdb=" N ALA H 309 " --> pdb=" O HIS H 305 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU H 310 " --> pdb=" O ALA H 306 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS H 313 " --> pdb=" O ALA H 309 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE H 317 " --> pdb=" O LYS H 313 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG H 322 " --> pdb=" O LYS H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 345 removed outlier: 3.623A pdb=" N TYR H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU H 342 " --> pdb=" O ARG H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 354 removed outlier: 3.961A pdb=" N ASN H 353 " --> pdb=" O ASN H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.513A pdb=" N ALA H 362 " --> pdb=" O PRO H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 376 Processing helix chain 'H' and resid 379 through 392 removed outlier: 3.811A pdb=" N ALA H 384 " --> pdb=" O ASP H 380 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN H 385 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR H 390 " --> pdb=" O GLU H 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA2, first strand: chain 'B' and resid 293 through 296 Processing sheet with id=AA3, first strand: chain 'C' and resid 293 through 296 Processing sheet with id=AA4, first strand: chain 'D' and resid 293 through 295 Processing sheet with id=AA5, first strand: chain 'E' and resid 293 through 296 Processing sheet with id=AA6, first strand: chain 'F' and resid 293 through 296 Processing sheet with id=AA7, first strand: chain 'G' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'H' and resid 293 through 295 1204 hydrogen bonds defined for protein. 3525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8503 1.34 - 1.46: 5451 1.46 - 1.58: 12102 1.58 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 26280 Sorted by residual: bond pdb=" N ASN D 71 " pdb=" CA ASN D 71 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.78e+00 bond pdb=" N ARG D 70 " pdb=" CA ARG D 70 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.28e-02 6.10e+03 6.01e+00 bond pdb=" N LYS A 19 " pdb=" CA LYS A 19 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.85e+00 bond pdb=" N ARG D 72 " pdb=" CA ARG D 72 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.35e-02 5.49e+03 5.25e+00 bond pdb=" N TYR B 214 " pdb=" CA TYR B 214 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.20e+00 ... (remaining 26275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 34417 1.13 - 2.26: 783 2.26 - 3.39: 105 3.39 - 4.51: 21 4.51 - 5.64: 10 Bond angle restraints: 35336 Sorted by residual: angle pdb=" N ILE F 163 " pdb=" CA ILE F 163 " pdb=" C ILE F 163 " ideal model delta sigma weight residual 112.96 109.08 3.88 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N LYS E 398 " pdb=" CA LYS E 398 " pdb=" C LYS E 398 " ideal model delta sigma weight residual 109.15 103.83 5.32 1.44e+00 4.82e-01 1.36e+01 angle pdb=" N LEU H 143 " pdb=" CA LEU H 143 " pdb=" C LEU H 143 " ideal model delta sigma weight residual 114.62 110.74 3.88 1.14e+00 7.69e-01 1.16e+01 angle pdb=" N ARG H 70 " pdb=" CA ARG H 70 " pdb=" C ARG H 70 " ideal model delta sigma weight residual 109.15 113.91 -4.76 1.44e+00 4.82e-01 1.09e+01 angle pdb=" N ARG C 331 " pdb=" CA ARG C 331 " pdb=" C ARG C 331 " ideal model delta sigma weight residual 111.82 108.31 3.51 1.16e+00 7.43e-01 9.15e+00 ... (remaining 35331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15268 17.96 - 35.92: 546 35.92 - 53.87: 80 53.87 - 71.83: 44 71.83 - 89.79: 70 Dihedral angle restraints: 16008 sinusoidal: 6528 harmonic: 9480 Sorted by residual: dihedral pdb=" CB GLU A 184 " pdb=" CG GLU A 184 " pdb=" CD GLU A 184 " pdb=" OE1 GLU A 184 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 189 " pdb=" CG GLU B 189 " pdb=" CD GLU B 189 " pdb=" OE1 GLU B 189 " ideal model delta sinusoidal sigma weight residual 0.00 89.78 -89.78 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU G 189 " pdb=" CG GLU G 189 " pdb=" CD GLU G 189 " pdb=" OE1 GLU G 189 " ideal model delta sinusoidal sigma weight residual 0.00 -89.65 89.65 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 16005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2782 0.038 - 0.076: 990 0.076 - 0.114: 71 0.114 - 0.152: 10 0.152 - 0.190: 3 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA TYR B 214 " pdb=" N TYR B 214 " pdb=" C TYR B 214 " pdb=" CB TYR B 214 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA LYS E 398 " pdb=" N LYS E 398 " pdb=" C LYS E 398 " pdb=" CB LYS E 398 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA LYS A 19 " pdb=" N LYS A 19 " pdb=" C LYS A 19 " pdb=" CB LYS A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 3853 not shown) Planarity restraints: 4544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 29 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C ASP A 29 " 0.071 2.00e-02 2.50e+03 pdb=" O ASP A 29 " -0.027 2.00e-02 2.50e+03 pdb=" N GLY A 30 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 72 " -0.195 9.50e-02 1.11e+02 8.74e-02 4.72e+00 pdb=" NE ARG D 72 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 72 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 72 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 72 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 39 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C MET C 39 " 0.025 2.00e-02 2.50e+03 pdb=" O MET C 39 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG C 40 " -0.009 2.00e-02 2.50e+03 ... (remaining 4541 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2665 2.75 - 3.28: 25628 3.28 - 3.82: 39031 3.82 - 4.36: 54267 4.36 - 4.90: 90687 Nonbonded interactions: 212278 Sorted by model distance: nonbonded pdb=" O GLY E 108 " pdb=" OH TYR E 130 " model vdw 2.207 3.040 nonbonded pdb=" O GLY H 108 " pdb=" OH TYR H 130 " model vdw 2.209 3.040 nonbonded pdb=" O GLY A 108 " pdb=" OH TYR A 130 " model vdw 2.212 3.040 nonbonded pdb=" O ASP F 218 " pdb=" OD1 ASP F 218 " model vdw 2.216 3.040 nonbonded pdb=" NH2 ARG G 70 " pdb=" OE1 GLU G 78 " model vdw 2.217 3.120 ... (remaining 212273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.860 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26280 Z= 0.129 Angle : 0.430 5.643 35336 Z= 0.278 Chirality : 0.035 0.190 3856 Planarity : 0.003 0.087 4544 Dihedral : 12.092 89.788 9944 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.10), residues: 3200 helix: -4.21 (0.05), residues: 1984 sheet: None (None), residues: 0 loop : -1.93 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 141 TYR 0.007 0.001 TYR A 150 PHE 0.008 0.001 PHE B 137 HIS 0.002 0.001 HIS A 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (26280) covalent geometry : angle 0.43041 / 0.28 (35336) hydrogen bonds : bond 0.30193 / 20.03 ( 1204) hydrogen bonds : angle 9.69550 / 6.69 ( 3525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.8416 (tpt) cc_final: 0.8011 (tpt) REVERT: A 354 MET cc_start: 0.8444 (mmt) cc_final: 0.8161 (mmp) REVERT: B 59 GLN cc_start: 0.7946 (tt0) cc_final: 0.7725 (tt0) REVERT: B 225 PHE cc_start: 0.8032 (m-10) cc_final: 0.7777 (m-10) REVERT: B 255 LYS cc_start: 0.8082 (tttt) cc_final: 0.7789 (mptt) REVERT: C 214 TYR cc_start: 0.6600 (t80) cc_final: 0.6156 (t80) REVERT: D 250 MET cc_start: 0.8434 (tpt) cc_final: 0.8041 (tpt) REVERT: D 317 PHE cc_start: 0.7766 (t80) cc_final: 0.7421 (t80) REVERT: D 354 MET cc_start: 0.8493 (mmt) cc_final: 0.8233 (mmp) REVERT: E 225 PHE cc_start: 0.7819 (m-80) cc_final: 0.7600 (m-10) REVERT: E 250 MET cc_start: 0.8458 (tpt) cc_final: 0.7950 (tpt) REVERT: E 317 PHE cc_start: 0.7664 (t80) cc_final: 0.7456 (t80) REVERT: E 354 MET cc_start: 0.8409 (mmt) cc_final: 0.8175 (mmp) REVERT: F 244 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7962 (tttp) REVERT: G 255 LYS cc_start: 0.8124 (tttt) cc_final: 0.7788 (mptt) REVERT: G 329 TYR cc_start: 0.7860 (t80) cc_final: 0.7633 (t80) REVERT: H 250 MET cc_start: 0.8378 (tpt) cc_final: 0.8011 (tpt) REVERT: H 317 PHE cc_start: 0.7798 (t80) cc_final: 0.7407 (t80) REVERT: H 354 MET cc_start: 0.8495 (mmt) cc_final: 0.8212 (mmp) REVERT: H 399 LEU cc_start: 0.8649 (mt) cc_final: 0.8429 (mt) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.2178 time to fit residues: 156.6364 Evaluate side-chains 320 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN B 147 HIS B 172 GLN C 147 HIS C 156 ASN C 172 GLN C 364 ASN C 385 GLN D 59 GLN D 258 GLN E 258 GLN F 133 ASN F 147 HIS F 172 GLN G 69 ASN G 147 HIS G 156 ASN H 59 GLN H 258 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112807 restraints weight = 32737.723| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.60 r_work: 0.3140 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 26280 Z= 0.126 Angle : 0.458 5.601 35336 Z= 0.254 Chirality : 0.035 0.131 3856 Planarity : 0.004 0.035 4544 Dihedral : 3.436 29.020 3592 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.83 % Allowed : 5.76 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.13), residues: 3200 helix: -1.83 (0.09), residues: 2056 sheet: None (None), residues: 0 loop : -1.80 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 40 TYR 0.013 0.001 TYR B 22 PHE 0.019 0.001 PHE A 317 HIS 0.003 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (26280) covalent geometry : angle 0.45825 / 0.25 (35336) hydrogen bonds : bond 0.05099 / 3.36 ( 1204) hydrogen bonds : angle 4.26210 / 2.93 ( 3525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 328 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8837 (tpt) cc_final: 0.8476 (tpt) REVERT: A 255 LYS cc_start: 0.7579 (mptt) cc_final: 0.7323 (mptt) REVERT: A 354 MET cc_start: 0.8831 (mmt) cc_final: 0.8433 (mmp) REVERT: B 59 GLN cc_start: 0.8087 (tt0) cc_final: 0.7872 (tt0) REVERT: B 255 LYS cc_start: 0.8437 (tttt) cc_final: 0.7740 (mptt) REVERT: B 258 GLN cc_start: 0.8236 (mt0) cc_final: 0.8006 (mm-40) REVERT: B 271 GLU cc_start: 0.7753 (mp0) cc_final: 0.7155 (mp0) REVERT: C 99 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8030 (mt-10) REVERT: C 225 PHE cc_start: 0.8343 (m-10) cc_final: 0.8026 (m-80) REVERT: C 244 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8354 (mttm) REVERT: C 271 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7180 (mp0) REVERT: C 364 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7313 (p0) REVERT: D 225 PHE cc_start: 0.8550 (m-10) cc_final: 0.8319 (m-80) REVERT: D 250 MET cc_start: 0.8773 (tpt) cc_final: 0.8374 (tpt) REVERT: D 317 PHE cc_start: 0.8157 (t80) cc_final: 0.7811 (t80) REVERT: E 180 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8513 (m-30) REVERT: E 225 PHE cc_start: 0.8383 (m-80) cc_final: 0.7898 (m-10) REVERT: E 250 MET cc_start: 0.8866 (tpt) cc_final: 0.8467 (tpt) REVERT: E 317 PHE cc_start: 0.8125 (t80) cc_final: 0.7819 (t80) REVERT: E 354 MET cc_start: 0.8813 (mmt) cc_final: 0.8425 (mmp) REVERT: F 244 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8288 (mttt) REVERT: G 255 LYS cc_start: 0.8380 (tttt) cc_final: 0.7855 (mptt) REVERT: G 258 GLN cc_start: 0.8242 (mt0) cc_final: 0.8021 (mm-40) REVERT: G 271 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7216 (mp0) REVERT: G 329 TYR cc_start: 0.8266 (t80) cc_final: 0.7793 (t80) REVERT: H 72 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.7962 (mtt-85) REVERT: H 225 PHE cc_start: 0.8502 (m-80) cc_final: 0.7950 (m-10) REVERT: H 250 MET cc_start: 0.8822 (tpt) cc_final: 0.8426 (tpt) REVERT: H 317 PHE cc_start: 0.8104 (t80) cc_final: 0.7758 (t80) outliers start: 23 outliers final: 13 residues processed: 347 average time/residue: 0.1946 time to fit residues: 104.9497 Evaluate side-chains 301 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 286 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain G residue 283 SER Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 385 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 88 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN B 156 ASN B 172 GLN C 172 GLN F 172 GLN H 258 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113364 restraints weight = 32828.085| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.61 r_work: 0.3151 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26280 Z= 0.095 Angle : 0.400 5.169 35336 Z= 0.217 Chirality : 0.035 0.132 3856 Planarity : 0.003 0.027 4544 Dihedral : 3.345 27.422 3592 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.27 % Allowed : 7.03 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3200 helix: -0.28 (0.11), residues: 2032 sheet: None (None), residues: 0 loop : -1.70 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 40 TYR 0.009 0.001 TYR B 22 PHE 0.017 0.001 PHE A 317 HIS 0.002 0.000 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.09 (26280) covalent geometry : angle 0.39994 / 0.22 (35336) hydrogen bonds : bond 0.03421 / 2.25 ( 1204) hydrogen bonds : angle 3.62266 / 2.48 ( 3525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 1.203 Fit side-chains REVERT: A 250 MET cc_start: 0.8827 (tpt) cc_final: 0.8454 (tpt) REVERT: A 255 LYS cc_start: 0.7578 (mptt) cc_final: 0.7339 (mptt) REVERT: A 354 MET cc_start: 0.8807 (mmt) cc_final: 0.8604 (mmp) REVERT: B 78 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 244 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8237 (mttm) REVERT: B 255 LYS cc_start: 0.8342 (tttt) cc_final: 0.7714 (mptt) REVERT: B 258 GLN cc_start: 0.8019 (mt0) cc_final: 0.7795 (mm-40) REVERT: C 214 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.7191 (t80) REVERT: C 225 PHE cc_start: 0.8370 (m-10) cc_final: 0.8143 (m-10) REVERT: C 244 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8353 (mttm) REVERT: D 225 PHE cc_start: 0.8486 (m-10) cc_final: 0.8233 (m-80) REVERT: D 250 MET cc_start: 0.8789 (tpt) cc_final: 0.8422 (tpt) REVERT: D 317 PHE cc_start: 0.8129 (t80) cc_final: 0.7783 (t80) REVERT: E 52 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8175 (mtp85) REVERT: E 180 ASP cc_start: 0.8795 (t0) cc_final: 0.8551 (m-30) REVERT: E 214 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: E 250 MET cc_start: 0.8867 (tpt) cc_final: 0.8489 (tpt) REVERT: E 317 PHE cc_start: 0.8128 (t80) cc_final: 0.7838 (t80) REVERT: E 382 TYR cc_start: 0.9064 (t80) cc_final: 0.8832 (t80) REVERT: F 52 ARG cc_start: 0.8276 (mtt90) cc_final: 0.8007 (mmm-85) REVERT: F 225 PHE cc_start: 0.8328 (m-10) cc_final: 0.8070 (m-80) REVERT: F 244 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8348 (mttt) REVERT: G 255 LYS cc_start: 0.8279 (tttt) cc_final: 0.7803 (mptt) REVERT: G 271 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7285 (mp0) REVERT: G 329 TYR cc_start: 0.8206 (t80) cc_final: 0.7728 (t80) REVERT: H 72 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.7953 (mtt-85) REVERT: H 214 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: H 250 MET cc_start: 0.8849 (tpt) cc_final: 0.8516 (tpt) REVERT: H 317 PHE cc_start: 0.8105 (t80) cc_final: 0.7740 (t80) outliers start: 35 outliers final: 21 residues processed: 328 average time/residue: 0.1910 time to fit residues: 97.8223 Evaluate side-chains 297 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 385 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 0.0980 chunk 271 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 172 GLN F 156 ASN F 172 GLN H 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110566 restraints weight = 32870.355| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.60 r_work: 0.3107 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 26280 Z= 0.172 Angle : 0.454 6.122 35336 Z= 0.240 Chirality : 0.037 0.140 3856 Planarity : 0.003 0.026 4544 Dihedral : 3.496 31.010 3592 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.74 % Allowed : 7.32 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 3200 helix: 0.25 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -1.57 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 40 TYR 0.013 0.001 TYR C 214 PHE 0.018 0.001 PHE A 317 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (26280) covalent geometry : angle 0.45393 / 0.24 (35336) hydrogen bonds : bond 0.03711 / 2.45 ( 1204) hydrogen bonds : angle 3.61686 / 2.47 ( 3525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 MET cc_start: 0.8930 (tpt) cc_final: 0.8573 (tpt) REVERT: A 354 MET cc_start: 0.8838 (mmt) cc_final: 0.8616 (mmp) REVERT: B 78 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 255 LYS cc_start: 0.8395 (tttt) cc_final: 0.7726 (mptt) REVERT: B 258 GLN cc_start: 0.8062 (mt0) cc_final: 0.7841 (mm-40) REVERT: B 364 ASN cc_start: 0.7602 (p0) cc_final: 0.7396 (p0) REVERT: C 214 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7383 (t80) REVERT: C 225 PHE cc_start: 0.8473 (m-10) cc_final: 0.8251 (m-10) REVERT: C 244 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8345 (mttt) REVERT: D 225 PHE cc_start: 0.8575 (m-10) cc_final: 0.8369 (m-80) REVERT: D 250 MET cc_start: 0.8848 (tpt) cc_final: 0.8374 (tpt) REVERT: D 317 PHE cc_start: 0.8145 (t80) cc_final: 0.7875 (t80) REVERT: E 180 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8616 (m-30) REVERT: E 214 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: E 250 MET cc_start: 0.8939 (tpt) cc_final: 0.8577 (tpt) REVERT: E 317 PHE cc_start: 0.8175 (t80) cc_final: 0.7866 (t80) REVERT: F 225 PHE cc_start: 0.8353 (m-10) cc_final: 0.8121 (m-10) REVERT: F 244 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8205 (mttt) REVERT: G 221 ASP cc_start: 0.7735 (t70) cc_final: 0.7254 (t0) REVERT: G 225 PHE cc_start: 0.8512 (m-80) cc_final: 0.8176 (m-80) REVERT: G 255 LYS cc_start: 0.8268 (tttt) cc_final: 0.7785 (mptt) REVERT: G 271 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7420 (mp0) REVERT: G 329 TYR cc_start: 0.8232 (t80) cc_final: 0.7769 (t80) REVERT: G 364 ASN cc_start: 0.7548 (p0) cc_final: 0.7318 (p0) REVERT: H 72 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.8089 (mtt-85) REVERT: H 214 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: H 225 PHE cc_start: 0.8545 (m-80) cc_final: 0.8256 (m-10) REVERT: H 250 MET cc_start: 0.8907 (tpt) cc_final: 0.8517 (tpt) REVERT: H 317 PHE cc_start: 0.8138 (t80) cc_final: 0.7871 (t80) outliers start: 48 outliers final: 37 residues processed: 325 average time/residue: 0.1950 time to fit residues: 98.8173 Evaluate side-chains 320 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 385 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 121 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 310 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 314 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 172 GLN F 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113989 restraints weight = 32452.686| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.56 r_work: 0.3149 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26280 Z= 0.087 Angle : 0.387 5.738 35336 Z= 0.207 Chirality : 0.034 0.130 3856 Planarity : 0.002 0.036 4544 Dihedral : 3.329 28.768 3592 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.41 % Allowed : 8.15 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3200 helix: 0.76 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -1.45 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 70 TYR 0.008 0.001 TYR C 214 PHE 0.018 0.001 PHE A 317 HIS 0.003 0.000 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (26280) covalent geometry : angle 0.38696 / 0.21 (35336) hydrogen bonds : bond 0.02944 / 1.94 ( 1204) hydrogen bonds : angle 3.34635 / 2.29 ( 3525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 291 time to evaluate : 1.020 Fit side-chains REVERT: A 70 ARG cc_start: 0.8511 (mtp-110) cc_final: 0.8075 (mtp-110) REVERT: A 250 MET cc_start: 0.8919 (tpt) cc_final: 0.8562 (tpt) REVERT: A 354 MET cc_start: 0.8816 (mmt) cc_final: 0.8582 (mmp) REVERT: B 78 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: B 225 PHE cc_start: 0.8411 (m-10) cc_final: 0.8144 (m-80) REVERT: B 244 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8335 (mttt) REVERT: B 255 LYS cc_start: 0.8477 (tttt) cc_final: 0.7877 (mptt) REVERT: B 364 ASN cc_start: 0.7658 (p0) cc_final: 0.7424 (p0) REVERT: C 214 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.7376 (t80) REVERT: C 244 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8338 (mttt) REVERT: D 250 MET cc_start: 0.8780 (tpt) cc_final: 0.8340 (tpt) REVERT: D 256 GLU cc_start: 0.8111 (pt0) cc_final: 0.7774 (pt0) REVERT: D 284 MET cc_start: 0.8578 (ttm) cc_final: 0.8071 (mtt) REVERT: D 317 PHE cc_start: 0.8110 (t80) cc_final: 0.7758 (t80) REVERT: E 16 ILE cc_start: 0.8991 (mm) cc_final: 0.8649 (mt) REVERT: E 180 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8507 (m-30) REVERT: E 214 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: E 250 MET cc_start: 0.8938 (tpt) cc_final: 0.8565 (tpt) REVERT: E 256 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: E 317 PHE cc_start: 0.8107 (t80) cc_final: 0.7842 (t80) REVERT: F 225 PHE cc_start: 0.8333 (m-10) cc_final: 0.8106 (m-10) REVERT: F 244 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8181 (mttt) REVERT: F 364 ASN cc_start: 0.7583 (p0) cc_final: 0.7352 (p0) REVERT: G 221 ASP cc_start: 0.7747 (t70) cc_final: 0.7097 (t0) REVERT: G 225 PHE cc_start: 0.8527 (m-80) cc_final: 0.8201 (m-80) REVERT: G 255 LYS cc_start: 0.8360 (tttt) cc_final: 0.7899 (mptt) REVERT: G 271 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7343 (mp0) REVERT: G 329 TYR cc_start: 0.8113 (t80) cc_final: 0.7692 (t80) REVERT: H 72 ARG cc_start: 0.8401 (mtt-85) cc_final: 0.8035 (mtt-85) REVERT: H 214 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: H 250 MET cc_start: 0.8882 (tpt) cc_final: 0.8479 (tpt) REVERT: H 317 PHE cc_start: 0.8086 (t80) cc_final: 0.7731 (t80) outliers start: 39 outliers final: 27 residues processed: 317 average time/residue: 0.1908 time to fit residues: 93.8120 Evaluate side-chains 305 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 39 MET Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 214 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN F 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111793 restraints weight = 32695.982| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.59 r_work: 0.3122 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26280 Z= 0.129 Angle : 0.413 10.779 35336 Z= 0.219 Chirality : 0.036 0.131 3856 Planarity : 0.003 0.041 4544 Dihedral : 3.381 29.312 3592 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.67 % Allowed : 8.30 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3200 helix: 0.92 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -1.36 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.011 0.001 TYR C 214 PHE 0.017 0.001 PHE A 317 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (26280) covalent geometry : angle 0.41296 / 0.22 (35336) hydrogen bonds : bond 0.03177 / 2.10 ( 1204) hydrogen bonds : angle 3.38695 / 2.31 ( 3525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 1.022 Fit side-chains REVERT: A 250 MET cc_start: 0.8947 (tpt) cc_final: 0.8567 (tpt) REVERT: A 354 MET cc_start: 0.8842 (mmt) cc_final: 0.8587 (mmp) REVERT: B 78 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: B 225 PHE cc_start: 0.8368 (m-10) cc_final: 0.8068 (m-10) REVERT: B 244 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8323 (mttt) REVERT: B 255 LYS cc_start: 0.8444 (tttt) cc_final: 0.7845 (mptt) REVERT: B 364 ASN cc_start: 0.7677 (p0) cc_final: 0.7432 (p0) REVERT: C 214 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7399 (t80) REVERT: C 225 PHE cc_start: 0.8357 (m-10) cc_final: 0.8098 (m-10) REVERT: C 244 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8340 (mttt) REVERT: D 250 MET cc_start: 0.8801 (tpt) cc_final: 0.8348 (tpt) REVERT: D 284 MET cc_start: 0.8654 (ttm) cc_final: 0.8427 (mtt) REVERT: D 317 PHE cc_start: 0.8119 (t80) cc_final: 0.7853 (t80) REVERT: E 16 ILE cc_start: 0.9060 (mm) cc_final: 0.8653 (mt) REVERT: E 180 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: E 214 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: E 250 MET cc_start: 0.8925 (tpt) cc_final: 0.8561 (tpt) REVERT: E 317 PHE cc_start: 0.8124 (t80) cc_final: 0.7844 (t80) REVERT: F 225 PHE cc_start: 0.8354 (m-10) cc_final: 0.8137 (m-10) REVERT: F 244 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8168 (mttt) REVERT: F 364 ASN cc_start: 0.7609 (p0) cc_final: 0.7368 (p0) REVERT: G 221 ASP cc_start: 0.7771 (t70) cc_final: 0.7021 (t0) REVERT: G 225 PHE cc_start: 0.8485 (m-80) cc_final: 0.8034 (m-80) REVERT: G 255 LYS cc_start: 0.8380 (tttt) cc_final: 0.7900 (mptt) REVERT: G 271 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7416 (mp0) REVERT: G 329 TYR cc_start: 0.8140 (t80) cc_final: 0.7699 (t80) REVERT: G 364 ASN cc_start: 0.7556 (p0) cc_final: 0.7332 (p0) REVERT: H 72 ARG cc_start: 0.8466 (mtt-85) cc_final: 0.8105 (mtt-85) REVERT: H 214 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: H 250 MET cc_start: 0.8864 (tpt) cc_final: 0.8427 (tpt) REVERT: H 256 GLU cc_start: 0.8138 (pt0) cc_final: 0.7917 (pt0) REVERT: H 317 PHE cc_start: 0.8099 (t80) cc_final: 0.7834 (t80) outliers start: 46 outliers final: 34 residues processed: 322 average time/residue: 0.1844 time to fit residues: 92.4869 Evaluate side-chains 319 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 280 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 385 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 18 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 187 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN F 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112308 restraints weight = 32559.225| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.65 r_work: 0.3123 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26280 Z= 0.109 Angle : 0.402 5.713 35336 Z= 0.214 Chirality : 0.035 0.131 3856 Planarity : 0.002 0.047 4544 Dihedral : 3.353 28.706 3592 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.41 % Allowed : 8.73 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3200 helix: 1.12 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -1.29 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 70 TYR 0.010 0.001 TYR C 214 PHE 0.016 0.001 PHE A 317 HIS 0.003 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (26280) covalent geometry : angle 0.40173 / 0.21 (35336) hydrogen bonds : bond 0.03043 / 2.00 ( 1204) hydrogen bonds : angle 3.33508 / 2.28 ( 3525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.8932 (tpt) cc_final: 0.8544 (tpt) REVERT: A 354 MET cc_start: 0.8833 (mmt) cc_final: 0.8565 (mmp) REVERT: B 78 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: B 225 PHE cc_start: 0.8381 (m-10) cc_final: 0.8059 (m-10) REVERT: B 244 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8309 (mttt) REVERT: B 255 LYS cc_start: 0.8419 (tttt) cc_final: 0.7808 (mptt) REVERT: B 364 ASN cc_start: 0.7683 (p0) cc_final: 0.7425 (p0) REVERT: C 214 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7443 (t80) REVERT: C 225 PHE cc_start: 0.8345 (m-10) cc_final: 0.8046 (m-10) REVERT: C 244 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8322 (mttt) REVERT: D 225 PHE cc_start: 0.8521 (m-80) cc_final: 0.8086 (m-10) REVERT: D 250 MET cc_start: 0.8790 (tpt) cc_final: 0.8396 (tpt) REVERT: D 317 PHE cc_start: 0.8101 (t80) cc_final: 0.7837 (t80) REVERT: E 16 ILE cc_start: 0.9053 (mm) cc_final: 0.8672 (mt) REVERT: E 180 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8581 (m-30) REVERT: E 214 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: E 250 MET cc_start: 0.8887 (tpt) cc_final: 0.8359 (tpt) REVERT: E 317 PHE cc_start: 0.8023 (t80) cc_final: 0.7737 (t80) REVERT: E 366 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7081 (t) REVERT: F 225 PHE cc_start: 0.8371 (m-10) cc_final: 0.8157 (m-10) REVERT: F 244 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8135 (mttt) REVERT: G 221 ASP cc_start: 0.7749 (t70) cc_final: 0.7335 (t0) REVERT: G 255 LYS cc_start: 0.8366 (tttt) cc_final: 0.7848 (mptt) REVERT: G 271 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7432 (mp0) REVERT: G 329 TYR cc_start: 0.8131 (t80) cc_final: 0.7660 (t80) REVERT: G 364 ASN cc_start: 0.7595 (p0) cc_final: 0.7352 (p0) REVERT: H 72 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8083 (mtt-85) REVERT: H 214 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: H 250 MET cc_start: 0.8887 (tpt) cc_final: 0.8520 (tpt) REVERT: H 317 PHE cc_start: 0.8092 (t80) cc_final: 0.7726 (t80) outliers start: 39 outliers final: 28 residues processed: 311 average time/residue: 0.1852 time to fit residues: 90.7621 Evaluate side-chains 306 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 385 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 249 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 115 optimal weight: 0.0000 chunk 110 optimal weight: 2.9990 chunk 305 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 0.0070 chunk 171 optimal weight: 1.9990 overall best weight: 0.9406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN F 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113380 restraints weight = 32558.199| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.59 r_work: 0.3153 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26280 Z= 0.092 Angle : 0.389 5.921 35336 Z= 0.209 Chirality : 0.035 0.130 3856 Planarity : 0.002 0.034 4544 Dihedral : 3.288 26.708 3592 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.34 % Allowed : 8.66 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3200 helix: 1.32 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -1.23 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 70 TYR 0.008 0.001 TYR C 214 PHE 0.019 0.001 PHE A 317 HIS 0.003 0.001 HIS G 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (26280) covalent geometry : angle 0.38902 / 0.21 (35336) hydrogen bonds : bond 0.02855 / 1.88 ( 1204) hydrogen bonds : angle 3.26737 / 2.24 ( 3525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.940 Fit side-chains REVERT: A 250 MET cc_start: 0.8910 (tpt) cc_final: 0.8527 (tpt) REVERT: A 354 MET cc_start: 0.8807 (mmt) cc_final: 0.8543 (mmp) REVERT: B 78 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: B 225 PHE cc_start: 0.8381 (m-10) cc_final: 0.8065 (m-10) REVERT: B 244 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8299 (mttt) REVERT: B 255 LYS cc_start: 0.8399 (tttt) cc_final: 0.7825 (mptt) REVERT: B 364 ASN cc_start: 0.7684 (p0) cc_final: 0.7426 (p0) REVERT: C 214 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7423 (t80) REVERT: C 225 PHE cc_start: 0.8332 (m-10) cc_final: 0.8038 (m-10) REVERT: C 244 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8338 (mttt) REVERT: D 225 PHE cc_start: 0.8475 (m-80) cc_final: 0.8018 (m-10) REVERT: D 250 MET cc_start: 0.8786 (tpt) cc_final: 0.8407 (tpt) REVERT: D 256 GLU cc_start: 0.7888 (pt0) cc_final: 0.7548 (tp30) REVERT: D 317 PHE cc_start: 0.8112 (t80) cc_final: 0.7860 (t80) REVERT: E 16 ILE cc_start: 0.9063 (mm) cc_final: 0.8721 (mt) REVERT: E 180 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8515 (m-30) REVERT: E 214 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: E 250 MET cc_start: 0.8872 (tpt) cc_final: 0.8411 (tpt) REVERT: E 317 PHE cc_start: 0.8030 (t80) cc_final: 0.7746 (t80) REVERT: E 366 CYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7084 (t) REVERT: F 225 PHE cc_start: 0.8405 (m-10) cc_final: 0.8196 (m-10) REVERT: F 244 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8148 (mttt) REVERT: G 221 ASP cc_start: 0.7733 (t70) cc_final: 0.6974 (t0) REVERT: G 225 PHE cc_start: 0.8424 (m-80) cc_final: 0.8060 (m-80) REVERT: G 255 LYS cc_start: 0.8350 (tttt) cc_final: 0.7887 (mptt) REVERT: G 271 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7394 (mp0) REVERT: G 297 ASP cc_start: 0.7924 (t70) cc_final: 0.7702 (t70) REVERT: G 329 TYR cc_start: 0.8105 (t80) cc_final: 0.7657 (t80) REVERT: G 364 ASN cc_start: 0.7588 (p0) cc_final: 0.7346 (p0) REVERT: H 72 ARG cc_start: 0.8405 (mtt-85) cc_final: 0.8043 (mtt-85) REVERT: H 214 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: H 250 MET cc_start: 0.8890 (tpt) cc_final: 0.8524 (tpt) REVERT: H 317 PHE cc_start: 0.8089 (t80) cc_final: 0.7742 (t80) outliers start: 37 outliers final: 28 residues processed: 311 average time/residue: 0.1741 time to fit residues: 85.0733 Evaluate side-chains 309 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 385 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 275 optimal weight: 0.9980 chunk 212 optimal weight: 0.0570 chunk 152 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 121 optimal weight: 0.3980 chunk 272 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 GLN F 172 GLN F 364 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113220 restraints weight = 32571.370| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.65 r_work: 0.3135 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26280 Z= 0.096 Angle : 0.390 6.052 35336 Z= 0.210 Chirality : 0.035 0.132 3856 Planarity : 0.002 0.030 4544 Dihedral : 3.277 25.242 3592 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.49 % Allowed : 8.59 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 3200 helix: 1.41 (0.12), residues: 2024 sheet: None (None), residues: 0 loop : -1.18 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 70 TYR 0.009 0.001 TYR C 214 PHE 0.019 0.001 PHE A 317 HIS 0.003 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (26280) covalent geometry : angle 0.39022 / 0.21 (35336) hydrogen bonds : bond 0.02865 / 1.89 ( 1204) hydrogen bonds : angle 3.25843 / 2.23 ( 3525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 1.097 Fit side-chains REVERT: A 70 ARG cc_start: 0.8683 (mtp-110) cc_final: 0.8331 (mtp-110) REVERT: A 250 MET cc_start: 0.8930 (tpt) cc_final: 0.8541 (tpt) REVERT: A 354 MET cc_start: 0.8830 (mmt) cc_final: 0.8577 (mmp) REVERT: B 78 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 225 PHE cc_start: 0.8387 (m-10) cc_final: 0.8064 (m-10) REVERT: B 244 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8299 (mttt) REVERT: B 255 LYS cc_start: 0.8382 (tttt) cc_final: 0.7807 (mptt) REVERT: B 364 ASN cc_start: 0.7687 (p0) cc_final: 0.7428 (p0) REVERT: C 214 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7417 (t80) REVERT: C 225 PHE cc_start: 0.8316 (m-10) cc_final: 0.8038 (m-10) REVERT: C 244 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8332 (mttt) REVERT: D 225 PHE cc_start: 0.8525 (m-80) cc_final: 0.8005 (m-10) REVERT: D 250 MET cc_start: 0.8781 (tpt) cc_final: 0.8395 (tpt) REVERT: D 256 GLU cc_start: 0.7733 (pt0) cc_final: 0.7461 (tp30) REVERT: D 317 PHE cc_start: 0.8113 (t80) cc_final: 0.7854 (t80) REVERT: E 16 ILE cc_start: 0.9001 (mm) cc_final: 0.8678 (mt) REVERT: E 180 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8543 (m-30) REVERT: E 214 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: E 250 MET cc_start: 0.8851 (tpt) cc_final: 0.8373 (tpt) REVERT: E 317 PHE cc_start: 0.8026 (t80) cc_final: 0.7729 (t80) REVERT: E 366 CYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7063 (t) REVERT: F 71 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8941 (p0) REVERT: F 225 PHE cc_start: 0.8422 (m-10) cc_final: 0.8197 (m-10) REVERT: F 244 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8153 (mttt) REVERT: G 225 PHE cc_start: 0.8393 (m-80) cc_final: 0.8182 (m-80) REVERT: G 255 LYS cc_start: 0.8357 (tttt) cc_final: 0.7867 (mptt) REVERT: G 271 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7419 (mp0) REVERT: G 329 TYR cc_start: 0.8123 (t80) cc_final: 0.7660 (t80) REVERT: G 364 ASN cc_start: 0.7619 (p0) cc_final: 0.7367 (p0) REVERT: H 214 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: H 250 MET cc_start: 0.8873 (tpt) cc_final: 0.8503 (tpt) REVERT: H 317 PHE cc_start: 0.8111 (t80) cc_final: 0.7751 (t80) outliers start: 41 outliers final: 31 residues processed: 316 average time/residue: 0.1840 time to fit residues: 91.0246 Evaluate side-chains 319 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 366 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 385 GLN Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 CYS Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 366 CYS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 385 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 242 optimal weight: 0.1980 chunk 259 optimal weight: 0.0010 chunk 304 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 144 optimal weight: 0.0070 chunk 62 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 268 optimal weight: 0.6980 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN C 156 ASN F 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117625 restraints weight = 32112.660| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.52 r_work: 0.3202 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.029 26280 Z= 0.068 Angle : 0.371 6.647 35336 Z= 0.202 Chirality : 0.034 0.130 3856 Planarity : 0.002 0.035 4544 Dihedral : 3.124 19.953 3592 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.01 % Allowed : 9.31 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 3200 helix: 1.65 (0.12), residues: 2040 sheet: None (None), residues: 0 loop : -1.07 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 70 TYR 0.009 0.001 TYR F 390 PHE 0.021 0.001 PHE A 317 HIS 0.002 0.000 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00140 / 0.07 (26280) covalent geometry : angle 0.37109 / 0.20 (35336) hydrogen bonds : bond 0.02388 / 1.56 ( 1204) hydrogen bonds : angle 3.11439 / 2.14 ( 3525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6400 Ramachandran restraints generated. 3200 Oldfield, 0 Emsley, 3200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 0.964 Fit side-chains REVERT: A 31 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7964 (mtm-85) REVERT: A 70 ARG cc_start: 0.8720 (mtp-110) cc_final: 0.8385 (mtp-110) REVERT: A 225 PHE cc_start: 0.8435 (m-80) cc_final: 0.8216 (m-10) REVERT: A 250 MET cc_start: 0.8891 (tpt) cc_final: 0.8554 (tpt) REVERT: A 354 MET cc_start: 0.8765 (mmt) cc_final: 0.8554 (mmp) REVERT: B 78 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: B 225 PHE cc_start: 0.8448 (m-10) cc_final: 0.8159 (m-10) REVERT: B 244 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8318 (mttt) REVERT: B 255 LYS cc_start: 0.8351 (tttt) cc_final: 0.8019 (mptt) REVERT: B 364 ASN cc_start: 0.7644 (p0) cc_final: 0.7386 (p0) REVERT: C 214 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.7336 (t80) REVERT: C 244 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8345 (mttt) REVERT: D 225 PHE cc_start: 0.8450 (m-80) cc_final: 0.7961 (m-10) REVERT: D 250 MET cc_start: 0.8681 (tpt) cc_final: 0.8399 (tpt) REVERT: D 256 GLU cc_start: 0.7506 (pt0) cc_final: 0.7097 (mm-30) REVERT: D 317 PHE cc_start: 0.8101 (t80) cc_final: 0.7784 (t80) REVERT: E 16 ILE cc_start: 0.8933 (mm) cc_final: 0.8698 (mt) REVERT: E 180 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: E 214 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: E 250 MET cc_start: 0.8816 (tpt) cc_final: 0.8397 (tpt) REVERT: E 317 PHE cc_start: 0.8078 (t80) cc_final: 0.7830 (t80) REVERT: F 225 PHE cc_start: 0.8491 (m-10) cc_final: 0.8239 (m-10) REVERT: F 244 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8165 (mttt) REVERT: G 255 LYS cc_start: 0.8456 (tttt) cc_final: 0.8018 (mptt) REVERT: G 329 TYR cc_start: 0.8058 (t80) cc_final: 0.7613 (t80) REVERT: G 364 ASN cc_start: 0.7597 (p0) cc_final: 0.7350 (p0) REVERT: H 214 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: H 250 MET cc_start: 0.8844 (tpt) cc_final: 0.8544 (tpt) REVERT: H 317 PHE cc_start: 0.8087 (t80) cc_final: 0.7771 (t80) outliers start: 28 outliers final: 17 residues processed: 317 average time/residue: 0.1918 time to fit residues: 94.6885 Evaluate side-chains 297 residues out of total 2760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 214 TYR Chi-restraints excluded: chain E residue 385 GLN Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 366 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 214 TYR Chi-restraints excluded: chain H residue 385 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 119 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 292 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 318 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 288 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 364 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114300 restraints weight = 32331.211| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.55 r_work: 0.3149 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26280 Z= 0.107 Angle : 0.402 5.920 35336 Z= 0.216 Chirality : 0.036 0.142 3856 Planarity : 0.003 0.035 4544 Dihedral : 3.202 20.329 3592 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.01 % Allowed : 9.64 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 3200 helix: 1.66 (0.12), residues: 2024 sheet: None (None), residues: 0 loop : -1.08 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 40 TYR 0.008 0.001 TYR C 214 PHE 0.021 0.001 PHE A 317 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (26280) covalent geometry : angle 0.40172 / 0.22 (35336) hydrogen bonds : bond 0.02841 / 1.87 ( 1204) hydrogen bonds : angle 3.21697 / 2.20 ( 3525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5677.45 seconds wall clock time: 98 minutes 29.89 seconds (5909.89 seconds total)